diff --git a/geneplexus/geneplexus.py b/geneplexus/geneplexus.py index 5ca5d2f..abaabcf 100755 --- a/geneplexus/geneplexus.py +++ b/geneplexus/geneplexus.py @@ -101,22 +101,22 @@ def __init__( "so this combination is not allowed.", ) - if ( - (self.sp_trn == "Fly" and self.gsc_trn == "Monarch") - or (self.sp_res == "Fly" and self.gsc_res == "Monarch") - ): + if (self.sp_trn == "Fly" and self.gsc_trn == "Monarch") or (self.sp_res == "Fly" and self.gsc_res == "Monarch"): raise FlyMonarchError( f"Fly has no annotations for Monarch. Use either Combined or GO for GSC", ) - - - if (self.gsc_trn == "Combined"): - logger.info(f"For the training species, {self.sp_trn}, the GSC is set to " - f"Combined and here: {config.COMBINED_CONTEXTS[self.sp_trn]}") - if (self.gsc_res == "Combined"): - logger.info(f"For the results species, {self.sp_res}, the GSC is set to " - f"Combined and here: {config.COMBINED_CONTEXTS[self.sp_res]}") - + + if self.gsc_trn == "Combined": + logger.info( + f"For the training species, {self.sp_trn}, the GSC is set to " + f"Combined and here: {config.COMBINED_CONTEXTS[self.sp_trn]}" + ) + if self.gsc_res == "Combined": + logger.info( + f"For the results species, {self.sp_res}, the GSC is set to " + f"Combined and here: {config.COMBINED_CONTEXTS[self.sp_res]}" + ) + # convert combined to GO so can read correct backend data if (self.sp_trn == "Fly") and (self.gsc_trn == "Combined"): self.gsc_trn = "GO" @@ -501,7 +501,7 @@ def fit_and_predict( if self.input_genes == None: raise NoPositivesError( f"There are no positive genes to train the model with.", - ) + ) self._get_pos_and_neg_genes() self.mdl_weights, self.probs, self.avgps = _geneplexus._run_sl( self.file_loc,